MK5 Microarray Data

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

Ontology Breakdown

Below is a table that can help you break down the effect of the gene alteration on the bioloigcal system. To create the table below we went over all the ontology terms and counted the number of times a gene was listed in that specific class, or one of its children. As can be expected, each class will differ in its behavior. Some will have a strong average regulation, but will contain very few genes, while others will be very large and broad classes that will have a lower average regulation, but which will whos an overall effect with many genes in many subgroups being affected.

The best strategy to analyze such classes is to a) filter out all the classes for which we have too little data (less than 5 affected genes on the micro array measurement). This can be done by writing '>5' in the 'Affected Genes' field. SEcondly we might also want to look at one specific ontology at first (click on 'biological process' in the table.

Once this is done we can sort the data properly by placing the 'Average Regulation' to the left (click on the green arrows) and the '% Affected Genes' as a second. We also want to sort them descending (the grey arrow should be pointing downward).

Now we can go investigate the data by first look at broadly affected classes ('Would Be Affected Genes'>60) and progressively lowering this value (to something like 'Would Be Affected Genes'>20)

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

Would Be Affected (#genes)	% Affected Genes	Average Regulation (ratio)	Class Size (#genes)	Class	Microarray Measured (#genes)	Class	Accession	affected

Results: HTML CSV LaTeX

Showing element 51 to 100 of 328 in total

Would Be Affected (#genes)	% Affected Genes	Average Regulation (ratio)	Class Size (#genes)	Class	Class
7	3.9735	2.267966568470001	164	transmembrane receptor protein tyrosine kinase signaling pathway	biological process
	3.6810	1.6151355107625325	184	Golgi apparatus part	cellular component
	3.5971	2.599970555305481	182	amine receptor activity	molecular function
	3.4682	3.243556241194407	191	alkali metal ion binding
	3.1746	1.8491697907447815	208	synapse	cellular component
	3.0928	2.506638288497925	238	microtubule
	3.0612	1.9925966064135234	216	cytoplasmic membrane-bound vesicle
				membrane-bound vesicle
	3.0303	1.3425244291623433	222	cell division	biological process
	2.2556	2.6377359429995217	315	voltage-gated ion channel activity	molecular function
	2.0833	1.9949067831039429	335	protein complex assembly	biological process
	2.0492	2.331825590133667	333	carbohydrate binding	molecular function
	2.0202	1.6523104111353557	337	response to DNA damage stimulus	biological process
	1.9608	2.2540424267450967	358	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
	1.8293	1.5113894144694011	388	amino acid and derivative metabolic process
	1.7595	1.5684048732121785	410	cytosol	cellular component
	1.5748	2.1708733439445496	421	organelle membrane
	1.5228	2.2601398825645447	464	monovalent inorganic cation transport	biological process
	1.4634	1.683560033639272	501	regulation of catalytic activity
8	4.2424	2.037709048816136	196	anion transporter activity	molecular function
	3.9773	2.6829177481787547	192	regulation of growth	biological process
	3.7234	1.8230999537876673	208	RNA splicing
	3.4146	1.6467143297195435	229	cell cycle phase
	3.3333	1.8456570080348425	249	RNA polymerase II transcription factor activity	molecular function
	2.5271	2.2348088707242693	321	nervous system development	biological process
	2.1605	2.6934666122709	379	nucleoplasm part	cellular component
	1.9663	1.6447297164372034	402	cell junction
	1.9608	2.2326475211552212	414	negative regulation of cellular metabolic process	biological process
	1.8421	2.158773183822632	428	response to endogenous stimulus
	1.7949	1.5929162161690849	463	amine metabolic process
	1.7157		484	nitrogen compound metabolic process
	1.6092	1.6290612050465174	527	regulation of a molecular function
	1.5748	1.4910563230514526	514	electron transport
9	6.3492	2.1655175536870956	142	protein amino acid dephosphorylation
	5.7143		158	dephosphorylation
	4.8000	2.9601402282714844	184	chromatin	cellular component
	4.1420	1.7680698462894984	221	metallopeptidase activity	molecular function
	3.8095	2.3925783783197403	230	enzyme linked receptor protein signaling pathway	biological process
	3.6145	2.5402226646741233	245	chromosome	cellular component
	3.4335	2.2164768129587173	264	organ morphogenesis	biological process
	3.1873	1.9443604201078415	295	electrochemical potential-driven transporter activity	molecular function
				porter activity
	2.9289	2.6086528982434953	318	inflammatory response	biological process
	2.8112	1.6669044835226876	327	iron ion binding	molecular function
	2.7888	1.4970425537654333	311	ATPase activity, coupled
	2.7778	2.043148085474968	323	transcription cofactor activity
	2.5078	2.4881605356931686	370	cation channel activity
		2.046714186668396		cell proliferation	biological process
	2.4922	2.8815125972032547	379	apoptosis
	2.4845		381	programmed cell death

Legend:
- The Average Regulation (ratio) is calculated only for the measured genes in this gene ontology term
- % Affected Genes is the % of genes in this gene ontology class that have been affected by the Mk5 alteration.
- Would Be Affected (#genes) represents how many genes of the overall class would have been affected if we measured each of them.
- The Class Size (#genes) counts the number of genes listed under the specific gene ontology term.
- Class is the GO class description.
- The Class refers to the ontology category, which can be molecular_function, biological_process or cellular_component.
- The Microarray Measured (#genes) lists how many genes of the specific ontology term were measured.
- Accession is the GO accession key.